Mesoporous materials have a wide range of applications in the fields of nanotechnology, biotechnology, information technology, and medicine, but historically, the resource materials used for their synthesis have been expensive. Natural silicate minerals are characterized by their abundance, low cost, and large SiO2 contents, making them an alternative silicon source for mesoporous silica. The objective of the present study was to determine the utility of natural chlorite as the source of Si for synthesizing hexagonal mesoporous silica materials (MCM-41). The natural chlorite was pretreated by acid leaching and calcination, followed by a hydrothermal reaction with cetyltrimethylammonium bromide (CTAB) as the template, and subsequent calcination to prepare MCM-41. The structures and the porosity of MCM-41 were characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), 29Si magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (29Si MAS NMR), and N2 adsorption–desorption measurements. The mechanism of structural evolution from natural chlorite to MCM-41 was investigated using these techniques. Calcination of chlorite results in amorphization and partial structural breakdown, while subsequent acid leaching dissolves the Mg and Al in the octahedral sheets to leave the Si–O framework as a silicon source. 29Si MAS NMR results revealed that the ratio of Q4/Q3 increased from 0.91 to 1.21 after hydrothermal synthesis of MCM-41 from leached chlorite, demonstrating more polymerization of the Si–O structure in MCM-41. The final MCM-41 products were amorphous SiO2, with a large surface area of 630 m2/g, a pore volume of 0.46 mL/g, and a narrow pore-size distribution of 2.8 nm. MCM-41 showed favorable adsorption toward methylene blue (MB) with a monolayer adsorption capacity of up to 302 mg/g, indicating potential for application in adsorption.